3D-partner: a web server to infer interacting partners and binding models. - Yung-Chiang Chen; Yu-Shu Lo; Wen-Chang Hsu; Jinn-Moon Yang (Nucleic Acids Res., 2007)

3D-interologs: A Protein-Protein Interacting Evolution Database across Multiple Species. - Jinn-Moon Yang; Yung-Chiang Chen; Yu-Shu Lo (IJCBS, 2009)

PPISearch: a web server for searching homologous protein-protein interactions across multiple species. - Chun-Chen Chen; Chun-Yu Lin 003; Yu-Shu Lo; Jinn-Moon Yang (Nucleic Acids Res., 2009)

Template-based scoring functions for visualizing biological insights of H-2Kb-peptide-TCR complexes. - I-Hsin Liu; Yu-Shu Lo; Jinn-Moon Yang (BIBM, 2010)

PCFamily: a web server for searching homologous protein complexes. - Yu-Shu Lo; Chun-Yu Lin 003; Jinn-Moon Yang (Nucleic Acids Res., 2010)

PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes. - I-Hsin Liu; Yu-Shu Lo; Jinn-Moon Yang (Nucleic Acids Res., 2011)

MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. - Chun-Yu Lin 003; Yi-Wei Lin; Shang-Wen Yu; Yu-Shu Lo; Jinn-Moon Yang (Nucleic Acids Res., 2012)

Inferring homologous protein-protein interactions through pair position specific scoring matrix. - Chun-Yu Lin 003; Yung-Chiang Chen; Yu-Shu Lo; Jinn-Moon Yang (BMC Bioinform., 2013)

Template-based scoring functions for visualising biological insights of H-2Kb-peptide-TCR complexes. - I-Hsin Liu; Yu-Shu Lo; Jinn-Moon Yang (Int. J. Data Min. Bioinform., 2013)

A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. - Sing-Han Huang; Yu-Shu Lo; Yong-Chun Luo; Yu-Yao Tseng; Jinn-Moon Yang (BMC Syst. Biol., 2018)

CoMI: consensus mutual information for tissue-specific gene signatures. - Sing-Han Huang; Yu-Shu Lo; Yong-Chun Luo; Yi-Hsuan Chuang; Jung-Yu Lee 001; Jinn-Moon Yang (BMC Bioinform., 2021)